Can bwa.kit start from bam file for HLA typing?

Question

[zengxi.hada]

Hi all,

I want to find HLA consensus sequence from bam file. Can I use bwa.kit to treat the bam file directly?

Thanks and best regards,
Michael

Answer 1

[afadda]

I have the same question. I tried this command but there was no sorted bam files or HLA typing. run-bwamem -o NA12878-hs38 -t 20 -H -s /Hsapiens/hs38DH/hs38DH.fa NA12878_2.fastq.gz NA12878_1.fastq.gz |sh

thanks,